Is there a strsplit method for DNAStringSet objects? I have a DNAStringSet object generated from the readFastq function (ShortRead package). In the middle of my reads is a barcode which I would like to use to split the reads into two reads (effectively treating the split read as paired-end reads).

I just added an strsplit method for XStringSet objects to the Biostrings packages. So you shouldn't need to convert to character vector anymore before calling strsplit(). This conversion can be expensive for an XStringSet object with tens of millions of sequences in it.

It's in Biostrings 2.43.8 (BioC devel only), which will propagate and become available via biocLite() in the next 24 hours or so.